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#!/usr/bin/env python
# -*- coding: utf-8 -*-
import json
import subprocess
import socket
from pybis import Openbis
def run(cmd, tmpdir="", params=[]):
completed_process = subprocess.run([cmd, tmpdir] + params, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
result = ''
if completed_process.stderr:
result += completed_process.stderr.decode('utf-8').strip()
if completed_process.stdout:
result += completed_process.stdout.decode('utf-8').strip()
print('-------------------' + cmd + '------------------- ' + str(tmpdir))
print(result)
return result
def test_obis(tmpdir):
# 0. pybis login
o = Openbis('https://localhost:8443', verify_certificates=False)
o.login('admin', 'admin', save_token=True)
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# 1. Global configuration
result = run('./01_global_config.sh', tmpdir)
config = json.loads(run('./00_get_config_global.sh'))
assert config['openbis_url'] == 'https://localhost:8443'
assert config['user'] == 'admin'
assert config['data_set_type'] == 'UNKNOWN'
assert config['verify_certificates'] == False
# 2. First commit
result = run('./02_first_commit_1_create_repository.sh', tmpdir)
assert '?? .obis/config.json' in result
assert '?? file' in result
result = run('./02_first_commit_2_commit.sh', tmpdir)
config = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data1'))
assert config['external_dms_id'].startswith('ADMIN-' + socket.gethostname().upper())
assert len(config['repository_id']) == 36
assert "Created data set {}.".format(config['data_set_id']) in result
# 3. Second commit
config_before = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data1'))
result = run('./03_second_commit_1_commit.sh', tmpdir)
config = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data1'))
assert config['data_set_id'] != config_before['data_set_id']
assert config['external_dms_id'].startswith('ADMIN-' + socket.gethostname().upper())
assert config['external_dms_id'] == config_before['external_dms_id']
assert config['repository_id'] == config_before['repository_id']
assert "Created data set {}.".format(config['data_set_id']) in result
result = run('./03_second_commit_2_git_annex_info.sh', tmpdir)
assert 'file: big_file' in result
assert 'key: SHA256E-s1000000--d29751f2649b32ff572b5e0a9f541ea660a50f94ff0beedfb0b692b924cc8025' in result
assert 'present: true' in result
# 4. Second repository
result = run('./04_second_repository.sh', tmpdir)
config_data1 = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data1'))
config = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data2'))
assert config['external_dms_id'].startswith('ADMIN-' + socket.gethostname().upper())
assert config['external_dms_id'] == config_data1['external_dms_id']
assert len(config['repository_id']) == 36
assert config['repository_id'] != config_data1['repository_id']
assert "Created data set {}.".format(config['data_set_id']) in result
# 5. Second external dms
result = run('./05_second_external_dms.sh', tmpdir)
config_data1 = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data1'))
config = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data_b/data3'))
assert config['external_dms_id'].startswith('ADMIN-' + socket.gethostname().upper())
assert config['external_dms_id'] != config_data1['external_dms_id']
assert len(config['repository_id']) == 36
assert config['repository_id'] != config_data1['repository_id']
assert "Created data set {}.".format(config['data_set_id']) in result
# 6. Error on first commit
result = run('./06_error_on_first_commit_1_error.sh', tmpdir)
assert 'Missing configuration settings for [\'object_id\', \'collection_id\'].' in result
result = run('./06_error_on_first_commit_2_status.sh', tmpdir)
assert '?? file' in result
result = run('./06_error_on_first_commit_3_commit.sh', tmpdir)
config = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data4'))
assert "Created data set {}.".format(config['data_set_id']) in result
# 7. Attach data set to a collection
result = run('./07_attach_to_collection.sh', tmpdir)
config = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data5'))
assert config['external_dms_id'].startswith('ADMIN-' + socket.gethostname().upper())
assert len(config['repository_id']) == 36
assert "Created data set {}.".format(config['data_set_id']) in result
# 8. Addref
result = run('./08_addref_1_success.sh', tmpdir)
config_data1 = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data1'))
config_data6 = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data6'))
assert config_data6 == config_data1
result = run('./08_addref_2_duplicate.sh', tmpdir)
assert 'DataSet already exists in the database' in result
result = run('./08_addref_3_non-existent.sh', tmpdir)
assert 'Invalid value' in result
# 9. Local clone
config_data2 = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data2'))
result = run('./09_local_clone.sh', tmpdir, [config_data2['data_set_id']])
config_data2_clone = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data_b/data2'))
assert config_data2_clone['external_dms_id'].startswith('ADMIN-' + socket.gethostname().upper())
assert config_data2_clone['external_dms_id'] != config_data2['external_dms_id']
del config_data2['external_dms_id']
del config_data2_clone['external_dms_id']
assert config_data2_clone == config_data2
# 11. Init analysis
result = run('./11_init_analysis_1_external.sh', tmpdir, [config_data2['data_set_id']])
config_data1 = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data1'))
config_analysis1 = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/analysis1'))
assert "Created data set {}.".format(config_analysis1['data_set_id']) in result
assert len(config_analysis1['repository_id']) == 36
assert config_analysis1['repository_id'] != config_data1['repository_id']
assert config_analysis1['data_set_id'] != config_data1['data_set_id']
result = run('./11_init_analysis_2_internal.sh', tmpdir)
config_analysis2 = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data1/analysis2'))
assert "Created data set {}.".format(config_analysis2['data_set_id']) in result
assert len(config_analysis2['repository_id']) == 36
assert config_analysis2['repository_id'] != config_data1['repository_id']
assert config_analysis2['data_set_id'] != config_data1['data_set_id']
result = run('./11_init_analysis_3_git_check_ignore.sh', tmpdir)
assert 'analysis2' in result
# 12. Metadata only commit
result = run('./12_metadata_only_1_commit.sh', tmpdir)
config = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data7'))
assert "Created data set {}.".format(config['data_set_id']) in result
result = run('./12_metadata_only_2_metadata_commit.sh', tmpdir)
config = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data7'))
assert "Created data set {}.".format(config['data_set_id']) in result
# 13. obis sync
result = run('./13_sync_1_git_commit_and_sync.sh', tmpdir)
config = json.loads(run('./00_get_config.sh', tmpdir + '/obis_data/data7'))
assert "Created data set {}.".format(config['data_set_id']) in result
result = run('./13_sync_2_only_sync.sh', tmpdir)
assert 'Nothing to sync' in result